Align alcohol dehydrogenase (EC 1.1.1.1); acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10) (characterized)
to candidate WP_011811972.1 VEIS_RS20705 aldehyde dehydrogenase family protein
Query= BRENDA::Q70YJ9 (885 letters) >NCBI__GCF_000015565.1:WP_011811972.1 Length = 482 Score = 231 bits (588), Expect = 1e-64 Identities = 152/462 (32%), Positives = 230/462 (49%), Gaps = 20/462 (4%) Query: 34 QKSKSDEEGLSSLKSTLNKAVAASKVFATYSQDQVDKIFRAAAEAA--NAARLPLAKMAV 91 + S + S + + +A AA ++ AT+SQ Q D AA A A LA++AV Sbjct: 2 EHSTAPSSAPSPITELVARARAAQRICATWSQAQADTAVTAAGWAIIEPARNRELAELAV 61 Query: 92 EETRMGVVEDKVIKNHFASEFVYSQYKNTKTCGLIAHDPISGYSKFAEPMGVIAGIIPTT 151 +T MG V+DKV+KNH + + ++ G+I DP G + A P+GV+ I P+T Sbjct: 62 ADTGMGCVQDKVLKNHRKTFGLLRDLHGARSVGVIGQDPARGIVEIARPVGVVCAITPST 121 Query: 152 NPTSTAIFKTLLALKTRNALVICPHPRAAKCTIAAAKVVLDAAVAAGAPADIITWIDSP- 210 NP +T K + ALK RNA+V+ P P+ + GAP D++ + P Sbjct: 122 NPGATPANKIINALKGRNAVVVAPSPKGWSTAARLIGFIHAQFDRIGAPRDLVQLLPGPI 181 Query: 211 SSLVSGALMKAPGSVLVLATGGPGMVRAVTLPA-PSLGVGAGNTPALIDETADIELAVNS 269 +G LM+ LV+ATG VRA P+ GVGAGN ++DETAD+ A Sbjct: 182 DKQATGELMRLCD--LVVATGSQANVRAAYASGTPAFGVGAGNVAGIVDETADVHAAAER 239 Query: 270 VLISKTFDNGVICASEQSIVAVDAVYDKVRAEFVRRGAYFLNEEEKVKVRKGIEKDGKLN 329 ++ SKTFDN C+SE S+V VDAV + A RGA L +K ++ + GKL+ Sbjct: 240 IVRSKTFDNATSCSSENSLVIVDAVRAPMLAALAERGAVMLTAAQKATLQALMWPGGKLS 299 Query: 330 ADIVGQPVAKLAQMFGITVPA-----------GAKVLIGEVSVVGKEEPLSQEKLSPILA 378 A ++GQ +A+ A G ++L+ G P S EKLSP+LA Sbjct: 300 AAVIGQSARSIAERAAALDDAQCAGWLALAATGPRILMVAEDGAGHGHPFSGEKLSPVLA 359 Query: 379 MYRSSDFNTALATTHKLIMFGGAGHTSVIYTHPDNRQNIEAFQAMAKTGRILVNSPSSQG 438 ++ + +F A A ++ GAGH+ + H + R++V+ S Sbjct: 360 IHGAQNFAAAAAMVERIYAHEGAGHS--VGLHSALPERALTLGLTLPVARVIVDQAHSI- 416 Query: 439 AIGGIYNQILAPSMTLGCGSWGGNIVSDNIGPLHLVNVKSVA 480 A GG ++ L S+++GCG+WG N SDN+ H +N+ V+ Sbjct: 417 ATGGSFDNGLPFSLSMGCGTWGKNSFSDNLNYRHYLNITRVS 458 Lambda K H 0.316 0.130 0.360 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 866 Number of extensions: 45 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 885 Length of database: 482 Length adjustment: 38 Effective length of query: 847 Effective length of database: 444 Effective search space: 376068 Effective search space used: 376068 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 54 (25.4 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory